Why don't you lay both harness' out and group what needs to be kept and what needs to be trashed together. Then based off of what needs to stay, start grouping the new harness into sections for your relays, grounds, switches, etc. It's going to take more than a couple hours to get it sorted out. The big thing here is getting everything needed into groups, once that's done, start putting it into your car and laying out where you want your relays, fuse panel, etc at. From there its just terminating your wires. I know sounds easier said than done, but its a start.

I have to start tearing into my body harness as well to run the Mazworx VVL intake manifold. If only I were closer we could help each other out. Would be a good learning process. Either way man, good luck with it, it's going to be a PITA.